"Under a Glass Moon" seems to be pretty forgotten...unfortunate, as it's an incredibly epic song that ranks up there with the likes of "Pull Me Under" and "Metropolis Part 1".
It may take a few listens to get into, but Awake is an amazing follow-up to Images and Words and can be a contender for the band's Magnum Opus.
"6:00". The opening drum beat let's you know you're in for good stuff.
"Innocence Faded" is perhaps the best vocal performance you'll hear from James Labrie. And if you think he can't sing well live after his vocal cord injury in the 90's, the live version from 2007's Score would like a word with you.
Also the entirety of Metropolis Part II: Scenes From A Memory.
"Overture 1928", while not the longest or flashiest song technically, does an amazing job of mashing up the melodies of the other songs on the album in a way that feels completely natural and is completely unnoticeable.
"Six Degrees of Inner Turbulence": One song, eight parts and 42 minutes of awesome. For maximum awesomeness, listen to all of the parts non-stop (if necessary, take a music-editing program and edit all the song parts together) for an absolutely epic joyride.
Off that album "The Glass Prison" deserves a special mention. The intro alone - which is admittedly quite long, but it is Dream Theater - is more awesome than some bands cram into one album.
The second act of their 20th anniversary concert features them playing with a full symphony orchestra. If you think DT isn't awesome per se, then wait until you hear "Six Degrees Of Inner Turbulence" and "Octavarium".
And for that matter, "Metropolis". It is the greatest possible way to finish an album ever.
"Constant Motion", one of Dream Theater's few singles, combines the speed of thrash metal with the technicality that is their hallmark, with a refrain worthy of power metal. "Forevermore! Into the night, blistering!"
"The Dark Eternal Night" is definitely one of the standout moments in Systematic Chaos. It has a groove that makes it an instant Ear Worm, while still sounding dark and heavy. During the verses, the distorted vocals portray the dark lyrics very well by sounding very much like an angry god who wants revenge in his people. Finally comes the amazing chorus and insane instrumental section. Mike Portnoy's stellar double-bass drumming also deserves special mention.
Black Clouds and Silver Linings boasts "The Best of Times": an anthem to fathers everywhere. Jordan Rudess' expressive piano parts and James Labrie's emotional vocals make this song a very powerful Tear Jerker.
The same album opens with "A Nightmare to Remember", which would not sound out of place on Train of Thought. The song boasts what is possibly the heaviest drumming in the band's discography. The serene-sounding middle part also deserves special mention with a chord progression that takes you to another dimension.
"Illumination Theory", especially the recurring Epic Riff. Also, it is very easy to let yourself drift off as you get lost in "Embracing Circle" section. That is until you are suddenly punched in the face by the "Pursuit of Truth" section, which is full of energy that continuously builds throughout the section until it finally climaxes at the beginning of the "Surrender, Trust, & Passion" section. It's all downhill from there. In a way, the song is like a movie with a well-defined plot.
"The Enemy Inside", like "Constant Motion", is a song that perfectly mixes Thrash Metal with Dream Theater's Signature Style. The song is very fast-paced with aggressive riffs at every turn, but there are still plenty of dynamic guitar and keyboard solos to still make it sound like Dream Theater. Mike Mangini's frantic drumming also adds to the intensity but doesn't overdo it.
That song is then followed by "The Looking Glass", which is an fantastic tribute to Rush. It has a main riff that sounds like something that the Canadian legends could have written. The metal-sounding verses provide a great contrast to the melodic chorus. John Petrucci's amazing guitar work (especially his very lyrical guitar solo) deserves special mention.